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WO2003048340A3 - Crystal structure of mitogen-activated protein kinase-activated protein kinase 2 and binding pockets thereof - Google Patents

Crystal structure of mitogen-activated protein kinase-activated protein kinase 2 and binding pockets thereof Download PDF

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Publication number
WO2003048340A3
WO2003048340A3 PCT/US2002/039070 US0239070W WO03048340A3 WO 2003048340 A3 WO2003048340 A3 WO 2003048340A3 US 0239070 W US0239070 W US 0239070W WO 03048340 A3 WO03048340 A3 WO 03048340A3
Authority
WO
WIPO (PCT)
Prior art keywords
protein kinase
activated protein
relates
mapkapk2
binding pockets
Prior art date
Application number
PCT/US2002/039070
Other languages
French (fr)
Other versions
WO2003048340A2 (en
Inventor
Wuyi Meng
Lovorka Swenson
Original Assignee
Vertex Pharma
Wuyi Meng
Lovorka Swenson
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Vertex Pharma, Wuyi Meng, Lovorka Swenson filed Critical Vertex Pharma
Priority to EP02799215A priority Critical patent/EP1461758A4/en
Priority to US10/497,767 priority patent/US20050261836A1/en
Priority to AU2002364141A priority patent/AU2002364141A1/en
Publication of WO2003048340A2 publication Critical patent/WO2003048340A2/en
Publication of WO2003048340A3 publication Critical patent/WO2003048340A3/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/12—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
    • C12N9/1205—Phosphotransferases with an alcohol group as acceptor (2.7.1), e.g. protein kinases
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/48—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving transferase
    • C12Q1/485—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving transferase involving kinase
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/573—Immunoassay; Biospecific binding assay; Materials therefor for enzymes or isoenzymes
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
    • G16B15/30—Drug targeting using structural data; Docking or binding prediction
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2299/00—Coordinates from 3D structures of peptides, e.g. proteins or enzymes
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment

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  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Organic Chemistry (AREA)
  • Biotechnology (AREA)
  • Physics & Mathematics (AREA)
  • General Health & Medical Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Immunology (AREA)
  • Biomedical Technology (AREA)
  • Biochemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Microbiology (AREA)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Hematology (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Urology & Nephrology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Food Science & Technology (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Cell Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Enzymes And Modification Thereof (AREA)
  • Peptides Or Proteins (AREA)

Abstract

The invention relates to crystalline molecules or molecular complexes that comprise binding pockets of mitogen activated protein kinase activated protein kinase 2 (MAPKAPK2) or its homologues. The invention also relates to crystals comprising MAPKAPK2. The present invention also relates to a computer comprising a data storage medium encoded with the structural coordinates of MAPKAPK2 binding pockets and methods of using a computer to evaluate the ability of a compound to bind to the molecule or molecular complex. This invention also relates to methods of using the structure coordinates to solve the structure of homologous proteins or protein complexes. In addition, this invention relates to methods of using the structure coordinates to screen for, design and optimize compounds, including agonists and antagonists, which bind to MAPKAPK2 or homologues thereof.
PCT/US2002/039070 2001-12-05 2002-12-05 Crystal structure of mitogen-activated protein kinase-activated protein kinase 2 and binding pockets thereof WO2003048340A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
EP02799215A EP1461758A4 (en) 2001-12-05 2002-12-05 Crystal structure of mitogen-activated protein kinase-activated protein kinase 2 and binding pockets thereof
US10/497,767 US20050261836A1 (en) 2001-12-05 2002-12-05 Crystal structure of mitogen-activated protein kinase-activated protein kinase 2 and binding pockets thereof
AU2002364141A AU2002364141A1 (en) 2001-12-05 2002-12-05 Crystal structure of mitogen-activated protein kinase-activated protein kinase 2 and binding pockets thereof

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US33751301P 2001-12-05 2001-12-05
US60/337,513 2001-12-05

Publications (2)

Publication Number Publication Date
WO2003048340A2 WO2003048340A2 (en) 2003-06-12
WO2003048340A3 true WO2003048340A3 (en) 2003-10-30

Family

ID=23320841

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2002/039070 WO2003048340A2 (en) 2001-12-05 2002-12-05 Crystal structure of mitogen-activated protein kinase-activated protein kinase 2 and binding pockets thereof

Country Status (4)

Country Link
US (1) US20050261836A1 (en)
EP (1) EP1461758A4 (en)
AU (1) AU2002364141A1 (en)
WO (1) WO2003048340A2 (en)

Families Citing this family (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20040005686A1 (en) * 2002-03-07 2004-01-08 Pharmacia Corporation Crystalline structure of human MAPKAP kinase-2
US7167802B2 (en) 2002-11-13 2007-01-23 Wyeth Methods for identifying agents that interact with MAP kinase activated protein kinase 2
GB0316271D0 (en) * 2003-07-11 2003-08-13 Univ Dundee Antimicrobial target
WO2005110476A1 (en) * 2004-05-13 2005-11-24 Daiichi Pharmaceutical Co., Ltd. Method of inhibiting telomerase activity and inhibitor
EP1851310B1 (en) * 2005-02-23 2011-01-26 Vertex Pharmaceuticals Incorporated Crystal structure of tak1-tab1
ATE555447T1 (en) 2006-06-14 2012-05-15 Vertex Pharma CRYSTAL STRUCTURE OF POLO-LIKE KINASE 3 (PLK3) AND BINDING POCKETS THEREOF
US8463652B2 (en) * 2009-06-25 2013-06-11 Tradeking Group, Inc. Method and system to facilitate on-line trading
US8463692B2 (en) * 2009-06-25 2013-06-11 Tradeking Group, Inc. Method and system to facilitate on-line trading
RS63581B1 (en) 2017-10-05 2022-10-31 Fulcrum Therapeutics Inc P38 kinase inhibitors reduce dux4 and downstream gene expression for the treatment of fshd
US10342786B2 (en) 2017-10-05 2019-07-09 Fulcrum Therapeutics, Inc. P38 kinase inhibitors reduce DUX4 and downstream gene expression for the treatment of FSHD
US11501853B2 (en) 2020-07-20 2022-11-15 Recursion Pharmaceuticals, Inc. Preemptible-based scaffold hopping
EP4244341A2 (en) * 2020-11-12 2023-09-20 Akttyva Therapeutics, Inc. Mk2 activating compounds for use in treating vascular leak and endothelial barrier disorders

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4886646A (en) * 1988-03-23 1989-12-12 The United States Of America As Represented By The Administrator Of The National Aeronautics And Space Administration Hanging drop crystal growth apparatus and method
US5096676A (en) * 1989-01-27 1992-03-17 Mcpherson Alexander Crystal growing apparatus
US5130105A (en) * 1990-10-23 1992-07-14 The United States Of America As Represented By The Administrator Of The National Aeronautics And Space Administration Protein crystal growth tray assembly
US5221410A (en) * 1991-10-09 1993-06-22 Schering Corporation Crystal forming device
US5884230A (en) * 1993-04-28 1999-03-16 Immunex Corporation Method and system for protein modeling
US5400741A (en) * 1993-05-21 1995-03-28 Medical Foundation Of Buffalo, Inc. Device for growing crystals
WO2002090524A2 (en) * 2001-02-28 2002-11-14 Merck & Co., Inc. Isolated nucleic acid molecules encoding a novel human signal transducing kinase-mapkap-2; encoded proteins, cells transformed therewith and uses thereof

Non-Patent Citations (7)

* Cited by examiner, † Cited by third party
Title
"Crystal structure of mapkap2", PROTEIN DATA BANK RECORD, 18 September 2002 (2002-09-18), XP002965438, Retrieved from the Internet <URL:http://www.rcsb.org/pdb/.> *
ENGEL K. ET AL.: "Constitutive activation of mitogen-activated protein kinase-activated protein kinase 2 by mutation of phosphorylation sites and an A-helix motif", THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 270, no. 45, November 1995 (1995-11-01), pages 27213 - 27221, XP002226892 *
HOLLAND P.M. ET AL.: "Protein modification: docking sites for kinases", CURRENT BIOLOGY, vol. 9, 1999, pages R329 - R331, XP002965435 *
MENG W.M. ET AL.: "Structure of mitogen-activated protein kinase-activated protein (MAPKAP) kinase 2 suggests a bifunctional switch that couples kinase activation with nuclear export", THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 277, no. 40, October 2002 (2002-10-01), pages 37401 - 37405, XP002965434 *
NEW L. ET AL.: "The p38 map kinase pathway and its biological function", TRENDS IN CARDIOVASCULAR MEDICINE, vol. 8, no. 5, July 1998 (1998-07-01), pages 220 - 228, XP002965437 *
PEARSON G. ET AL.: "Mitogen activated protein (MAP) kinase pathways: regulation and physiological functions", ENDOCRINE REVIEWS, vol. 22, no. 2, 2001, pages 153 - 183, XP002235969 *
ZU Y.-L. ET AL.: "Characterization of an autoinhibitory domain in human mitogen activated protein kinase activated protein kinase 2", THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 270, no. 1, January 1995 (1995-01-01), pages 202 - 206, XP002965436 *

Also Published As

Publication number Publication date
AU2002364141A8 (en) 2003-06-17
AU2002364141A1 (en) 2003-06-17
EP1461758A4 (en) 2005-10-05
WO2003048340A2 (en) 2003-06-12
US20050261836A1 (en) 2005-11-24
EP1461758A2 (en) 2004-09-29

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